8OHV

Crystal structure of Beta-glucuronidase from Acidobacterium capsulatum in complex with glucuronic acid configured 3-geminal diol iminosugar inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7PSH 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.5 M AmSO4 1 M LiSO4 0.1 M Trisodium Citrate
Crystal Properties
Matthews coefficientSolvent content
2.3848.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.037α = 90
b = 42.614β = 99.417
c = 140.141γ = 90
Symmetry
Space GroupI 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2021-02-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.979499DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.540.7561000.999116.476979
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.530.545

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1.540.75676978386199.9490.20.19890.223122.124
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-0.2640.5320.871-0.743
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.899
r_dihedral_angle_4_deg20.262
r_dihedral_angle_3_deg14.187
r_dihedral_angle_1_deg6.846
r_lrange_other5.825
r_lrange_it5.824
r_scangle_it4.881
r_scangle_other4.881
r_scbond_it3.269
r_scbond_other3.269
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.899
r_dihedral_angle_4_deg20.262
r_dihedral_angle_3_deg14.187
r_dihedral_angle_1_deg6.846
r_lrange_other5.825
r_lrange_it5.824
r_scangle_it4.881
r_scangle_other4.881
r_scbond_it3.269
r_scbond_other3.269
r_mcangle_it2.867
r_mcangle_other2.867
r_mcbond_it2.037
r_mcbond_other2.032
r_angle_refined_deg1.771
r_angle_other_deg1.524
r_nbd_other0.222
r_nbd_refined0.212
r_symmetry_nbd_other0.19
r_nbtor_refined0.176
r_symmetry_xyhbond_nbd_refined0.14
r_symmetry_nbd_refined0.109
r_xyhbond_nbd_refined0.099
r_symmetry_nbtor_other0.087
r_chiral_restr0.086
r_bond_refined_d0.011
r_gen_planes_refined0.011
r_chiral_restr_other0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3417
Nucleic Acid Atoms
Solvent Atoms182
Heterogen Atoms17

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing